14.1.18. crate_anon.anonymise.make_demo_database

crate_anon/anonymise/make_demo_database.py

Copyright (C) 2015, University of Cambridge, Department of Psychiatry. Created by Rudolf Cardinal (rnc1001@cam.ac.uk).

This file is part of CRATE.

CRATE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CRATE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with CRATE. If not, see <https://www.gnu.org/licenses/>.

Makes a test database (from tiny to large) for anonymisation testing.

See also:

After anonymisation, check with:

SELECT * FROM anonymous_output.notes WHERE brcid IN (
    SELECT brcid
    FROM anonymous_mapping.secret_map
    WHERE patient_id < 2
);
SELECT * FROM test.patients WHERE patient_id < 2;

class crate_anon.anonymise.make_demo_database.BlobDoc(patient, filename, blob_datetime)[source]

SQLAlchemy ORM class for fictional binary documents.

__init__(patient, filename, blob_datetime)

Parameters

patient – corresponding Patient object
filename – filename containing the binary document to load and store in the database
blob_datetime – date/time value to give this BLOB

class crate_anon.anonymise.make_demo_database.EnumColours(value)[source]: A silly enum, for testing.

class crate_anon.anonymise.make_demo_database.FilenameDoc(**kwargs)[source]

SQLAlchemy ORM class for a table containing the filenames of binary documents.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class crate_anon.anonymise.make_demo_database.Note(**kwargs)[source]

SQLAlchemy ORM class for fictional notes.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class crate_anon.anonymise.make_demo_database.Patient(**kwargs)[source]

SQLAlchemy ORM class for fictional patients.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

crate_anon.anonymise.make_demo_database.coin(p: float = 0.5) → bool[source]: Biased coin toss. Returns True with probability p.

crate_anon.anonymise.make_demo_database.compile_blob_mysql(type_: TypeEngine, compiler: SQLCompiler, **kw) → str[source]

Provides a custom type for the SQLAlchemy LargeBinary type under MySQL, by using LONGBLOB (which overrides the default of BLOB).

MySQL: https://dev.mysql.com/doc/refman/5.7/en/storage-requirements.html

TINYBLOB: up to 2^8 bytes
BLOB: up to 2^16 bytes = 64 KiB
MEDIUMBLOB: up to 2^24 bytes = 16 MiB  <-- minimum for docs
LONGBLOB: up to 2^32 bytes = 4 GiB

VARBINARY: up to 65535 = 64 KiB

SQL Server: https://msdn.microsoft.com/en-us/library/ms188362.aspx

BINARY: up to 8000 bytes = 8 KB
VARBINARY(MAX): up to 2^31 - 1 bytes = 2 GiB <-- minimum for docs
IMAGE: deprecated; up to 2^31 - 1 bytes = 2 GiB
    https://msdn.microsoft.com/en-us/library/ms187993.aspx

SQL Alchemy:

_Binary: base class
LargeBinary: translates to BLOB in MySQL
VARBINARY, as an SQL base data type
dialects.mysql.base.LONGBLOB
dialects.mssql.base.VARBINARY

Therefore, we can take the LargeBinary type and modify it.

crate_anon.anonymise.make_demo_database.main() → None[source]: Command-line processor. See command-line help.